Genomics of Imperata cylindrica

Imperata cylindrica (Cogongrass, Speargrass), a noxious weed in at least 73 countries, has invaded over 1.5 million acres in the southern United States. Current control measures of herbicide application are too costly for the economically-depressed, rural southern US. Moreover, herbicides fail to control the spread of this species. Cogongrass has been identified as an alternate host for Rice Yellow Mottle Virus and for Imperata Yellow Mottle Virus, a maize pathogen, and thus constitutes a significant threat to domestic and global food security. Cogongrass is a compelling example of a species for which biological controls should be developed.

We present a novel use of genomics to characterize an invasive plant species. Using Digital Genotyping (DG), a high throughput, reduced representation, genotyping-by-sequencing technology developed for C4 grasses, we have sequenced over 1000 samples of domestic and international samples of Imperata. The genome of Imperata has not been sequenced to date, therefore, we employed the close relative, Sorghum bicolor, as a proxy reference genome to facilitate single nucleotide polymorphism (SNP) discovery. Through DG, comparative genomics and GIS data associated with each sample, we have produced a high-resolution global population-genetic profile, enabling genotype matching of domestic and international samples of this highly clonal species. This data allowed us to pinpoint specific regions in Asia for biological control exploration. This year, over 90 potential host-specific controls were collected across Japan and The Philippines. The resources we have assembled will set the framework for pursuing the genetic architecture underlying the extreme fitness of Imperata cylindrica.